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https://github.com/genome/genome
23 March 2024, 19:04:16 UTC
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Revision Author Date Message Commit Date
720cebf APipe Tester 08 March 2014, 13:17:17 UTC Updated `genome` tab completion. 08 March 2014, 13:17:17 UTC
28e2220 apregier 07 March 2014, 20:32:18 UTC Merge branch 'my_annotation' into gb_master 07 March 2014, 20:32:18 UTC
9dd8de3 apregier 07 March 2014, 20:30:45 UTC Added new processing profile parameters to import/export test 07 March 2014, 20:31:21 UTC
75e24f3 dmorton 07 March 2014, 18:54:00 UTC Bugfix: Missed a call to _capture 07 March 2014, 18:54:00 UTC
fe7245c dmorton 07 March 2014, 17:04:28 UTC Bugfix: Name of function on FeatureList changed 07 March 2014, 17:04:28 UTC
700188a dmorton 07 March 2014, 17:02:17 UTC Move lazy-loading of IPC::Sysem::Simple into Genome::Sys 07 March 2014, 17:04:08 UTC
9276a15 Anthony Brummett 05 March 2014, 21:58:47 UTC Tighten up the new Nessy locks When locking, get the Nessy lock first, then the file-based lock The Nessy lock adapter now understands the 'wait_on_self', 'block_sleep' and 'max_try' options. lock_resource and unlock_resource generate error_message()s when unexpected things happen, like if we can get a Nessy lock but not a file-based lock. 07 March 2014, 14:34:25 UTC
17085ae Anthony Brummett 27 February 2014, 20:28:12 UTC Hook into Nessy for locking Use the Nessy locking server if the env var GENOME_NESSY_SERVER is set. The existing disk-based locks are still used primarily. When the old-style lock succeeds, then it calls the equivalent Nessy lock method. 07 March 2014, 14:34:24 UTC
58d9ab9 Anthony Brummett 04 March 2014, 20:03:51 UTC Extract methods to parse args and handle the meat of file-based locking 07 March 2014, 14:34:23 UTC
f99d83e Susanna Siebert 06 March 2014, 18:47:59 UTC restrict_to_target_regions and target_regions also need to be processing profile params 07 March 2014, 14:11:27 UTC
06757a9 APipe Tester 07 March 2014, 14:00:07 UTC updated workflow submodule to 1951cac 07 March 2014, 14:00:07 UTC
873de14 APipe Tester 07 March 2014, 13:17:36 UTC Updated `gmt` tab completion. 07 March 2014, 13:17:36 UTC
4d00472 APipe Tester 07 March 2014, 13:16:51 UTC Updated `genome` tab completion. 07 March 2014, 13:16:51 UTC
4aaacb7 APipe Tester 07 March 2014, 13:15:14 UTC Updated class browser cache. 07 March 2014, 13:15:14 UTC
65a7ce7 Kyung Kim 07 March 2014, 04:16:52 UTC Tool to filter duplicate sequences in reads 07 March 2014, 04:16:52 UTC
36feea3 Dave Larson 07 March 2014, 03:50:44 UTC add a little bit of feedback. 07 March 2014, 03:50:50 UTC
b00be1c Avinash Ramu 06 March 2014, 23:58:18 UTC don't use hard-coded paths for db's The files required for annotation are accessed using a Genome::Db method. 06 March 2014, 23:58:18 UTC
ef4e8c8 APipe Tester 06 March 2014, 23:15:15 UTC updated workflow submodule to c8fb4b2 06 March 2014, 23:15:15 UTC
f851937 apregier 06 March 2014, 23:14:46 UTC Merge branch 'my_annotation' into gb_master 06 March 2014, 23:14:46 UTC
506e425 apregier 06 March 2014, 23:09:31 UTC Make analysis-project optional for id import 06 March 2014, 23:10:08 UTC
7a1d43a apregier 06 March 2014, 23:08:16 UTC New nomenclature 06 March 2014, 23:10:05 UTC
97dcf3b Gabriel Sanderson 06 March 2014, 22:47:12 UTC Fixed a typo in the grep. Use capture instead of backticks to make sure it runs. Test it. 06 March 2014, 22:47:20 UTC
f4aa19f dmorton 06 March 2014, 22:25:12 UTC Lean on new FeatureList functionality in 'gmt vcf cross-sample' 06 March 2014, 22:46:30 UTC
b65a56c dmorton 06 March 2014, 21:24:26 UTC Lean on new FeatureList functionality in CCSVCF 06 March 2014, 22:46:30 UTC
58f1400 APipe Tester 06 March 2014, 22:33:56 UTC updated jenkins submodule to 5e98e09 06 March 2014, 22:33:56 UTC
335e5c6 Gabriel Sanderson 06 March 2014, 21:51:46 UTC Added resolve_roi_for_reference, which checks references before converting the bed file. Also do a basic check for "chr" chromosomes if they do not belong. 06 March 2014, 21:58:14 UTC
c57c419 Gabriel Sanderson 06 March 2014, 20:36:18 UTC target_bed checks to make sure it exists when accessed 06 March 2014, 21:58:13 UTC
1702189 Gabriel Sanderson 06 March 2014, 20:15:49 UTC Removed caching -- using software results now. 06 March 2014, 21:58:12 UTC
7b18010 Gabriel Sanderson 06 March 2014, 20:13:20 UTC Remove old TODO 06 March 2014, 21:58:10 UTC
efbbf50 Gabriel Sanderson 06 March 2014, 20:12:28 UTC Start using ConvertedBedResult instead of directly calling convert_bed 06 March 2014, 21:58:08 UTC
84d56e0 Gabriel Sanderson 06 March 2014, 02:11:32 UTC Added ConvertedBedResult to act as a software result for feature list bed files, once they are converted to another reference sequence. 06 March 2014, 21:58:06 UTC
2c7ca6a Thomas Mooney 06 March 2014, 20:28:30 UTC Fix typo: symlinke => symlink. 06 March 2014, 20:28:30 UTC
c844d7e dmorton 06 March 2014, 19:25:42 UTC remove die condition in vcf Backfill When we create vcf files from mpileup (in dv2) the converter does not put in a AD field and always leaves the BQ field set to '.' so we cannot possibly satisfy this condition. The code will just accept the newly discovered evidence for alts at this site. 06 March 2014, 19:30:51 UTC
b5f5a9d apregier 06 March 2014, 18:17:26 UTC Merge branch 'my_annotation' into gb_master 06 March 2014, 18:17:26 UTC
646b6f2 apregier 06 March 2014, 18:15:13 UTC Restore Job::Iterator package 06 March 2014, 18:16:30 UTC
0d251f0 Jim Weible 06 March 2014, 16:20:47 UTC note the annoation-version param is deprecated 06 March 2014, 16:20:47 UTC
19db5d7 Jim Weible 06 March 2014, 16:20:25 UTC handle annotation data set correctly in the test 06 March 2014, 16:20:25 UTC
edce14c Jim Weible 28 February 2014, 15:57:28 UTC Revert "Revert "do the right thing with the copycat annotation"" This reverts commit e06fc4e36dd8092fee0b1f22eb730ce3a5a6ac8d. 06 March 2014, 14:03:59 UTC
5fe2924 Jim Weible 28 February 2014, 15:57:26 UTC Revert "Revert "write our temp files to a reasonable place"" This reverts commit 3cd0df3a9b7e6715ec16ea6cf02ef7706778bbbb. 06 March 2014, 14:03:58 UTC
a122cae Jim Weible 28 February 2014, 15:57:24 UTC Revert "Revert "fix up some copy pasta error messages"" This reverts commit 6055056b0dba9c93204e845b582a5f213384acdd. 06 March 2014, 14:03:58 UTC
8767185 Jim Weible 28 February 2014, 15:57:13 UTC Revert "Revert "create a dummy expected output file as standard for cnv detectors"" This reverts commit 5abef98c7ca3d5782240449500339ead9fc2b03e. 06 March 2014, 14:03:57 UTC
6cf65de APipe Tester 06 March 2014, 13:17:37 UTC Updated `gmt` tab completion. 06 March 2014, 13:17:37 UTC
1875d90 APipe Tester 06 March 2014, 13:16:49 UTC Updated `genome` tab completion. 06 March 2014, 13:16:49 UTC
76987f0 APipe Tester 06 March 2014, 13:15:12 UTC Updated class browser cache. 06 March 2014, 13:15:12 UTC
f99c881 apregier 06 March 2014, 02:32:45 UTC Merge branch 'my_annotation' into gb_master 06 March 2014, 02:32:45 UTC
1a02f30 apregier 06 March 2014, 02:31:01 UTC Don't break /gsc/bin/perl 06 March 2014, 02:31:01 UTC
430fa0e apregier 06 March 2014, 02:03:12 UTC Merge branch 'my_annotation' into gb_master 06 March 2014, 02:03:12 UTC
a738e51 apregier 05 March 2014, 22:58:54 UTC Check that builds weren't succeeded in between. 05 March 2014, 22:58:54 UTC
9a5d121 apregier 05 March 2014, 22:25:19 UTC Update cron 05 March 2014, 22:25:41 UTC
3816181 apregier 05 March 2014, 22:23:36 UTC Use exceptions 05 March 2014, 22:25:41 UTC
b096bb7 apregier 04 March 2014, 21:59:22 UTC Rewrite scan cron 05 March 2014, 22:25:40 UTC
b2b82c6 APipe Tester 05 March 2014, 22:22:16 UTC updated jenkins submodule to 8a9a322 05 March 2014, 22:22:16 UTC
609cb07 dmorton 05 March 2014, 20:51:17 UTC Stop trying to parse snv_detection_strategy for samtools info This was problematic for builds that had processing profiles that specified 'mpileup -BuDS' for instance since 'mpileup' is not a samtools pileup param. 05 March 2014, 20:53:09 UTC
ec22ef5 Chris Miller 05 March 2014, 20:24:32 UTC updated stderr message to make sense 05 March 2014, 20:24:32 UTC
0f66486 Chris Miller 05 March 2014, 20:02:47 UTC fixing hash reference bug 05 March 2014, 20:08:59 UTC
3d6b4fd Chris Miller 05 March 2014, 19:36:38 UTC adding reference-transcripts option to specify one that differs from the model 05 March 2014, 20:08:58 UTC
61bd7e1 Susanna Siebert 05 March 2014, 19:34:19 UTC need to use Test::More instead of Genome::Model::SomaticVariation::Command::TestHelpers 05 March 2014, 19:34:19 UTC
d90d1d7 Susanna Siebert 05 March 2014, 19:09:12 UTC fixed package name 05 March 2014, 19:22:40 UTC
f1ac2c9 Thomas Mooney 05 March 2014, 16:42:54 UTC Only examine the first 1000 lines of the BAM when discerning read length. Otherwise for large BAMs this process takes a *long* time without much gain in accuracy. 05 March 2014, 16:42:54 UTC
1ddec2d Susanna Siebert 05 March 2014, 15:12:02 UTC don't compare the output from reports/review.xml as that file will always be different 05 March 2014, 15:12:29 UTC
8ab9897 APipe Tester 05 March 2014, 14:00:26 UTC updated workflow submodule to 4332dce 05 March 2014, 14:00:26 UTC
2523308 Nathaniel Nutter 05 March 2014, 05:16:37 UTC pull up fetch utility 05 March 2014, 05:16:37 UTC
393784e Nathaniel Nutter 05 March 2014, 04:56:13 UTC refactor URL fetching Extracted similar code into a utility function and updated to use File::Fetch instead of shelling out to curl. 05 March 2014, 04:56:13 UTC
ca74757 Nathaniel Nutter 05 March 2014, 01:14:35 UTC delegate to local version if it is found If we update either of these normally people would't get them until they get deployed. With this delegation code in there it will try use the fact that someone is in a Git repo with the same executable to delegate to it. 05 March 2014, 01:15:47 UTC
5d93215 Nathaniel Nutter 04 March 2014, 21:41:57 UTC fixes RT #98012, shellcmd STDERR/STDOUT FCGI bug 05 March 2014, 00:49:37 UTC
0d56bbc Nathaniel Nutter 04 March 2014, 20:10:58 UTC can't use non-string variables in 3-argument open due to FCGI (I think) FCGI ties STDERR, STDOUT, and STDIN which overrides open calls. In the case of a 3-argument open it does: eval("$rc = open($_[0], $_[1], $_[2])"); Which means that the variables can't be "the normal 'reference to a glob'" as is supposed to be the case. 05 March 2014, 00:49:36 UTC
bbd8827 Nathaniel Nutter 04 March 2014, 20:08:01 UTC use parens 05 March 2014, 00:49:35 UTC
25785ae Nathaniel Nutter 04 March 2014, 20:06:28 UTC only backup STDOUT/STDERR if redirected 05 March 2014, 00:49:33 UTC
b26285a Nathaniel Nutter 04 March 2014, 23:58:57 UTC reload allocations so they are no longer archived in memory 05 March 2014, 00:34:39 UTC
3ab93cd Nathaniel Nutter 05 March 2014, 00:33:36 UTC test's models were updated with new processing profile (DV2 bug fix) 05 March 2014, 00:34:38 UTC
d6bc402 Nathaniel Nutter 04 March 2014, 23:40:24 UTC updated expected output for new GENOME_TEST_INPUTS Changed from/to: https://gscweb.gsc.wustl.edu file:// 04 March 2014, 23:45:55 UTC
36fde30 Nathaniel Nutter 04 March 2014, 23:28:55 UTC disable test for one week b/c of disk maintenance 04 March 2014, 23:45:54 UTC
64a4ad5 Nathaniel Nutter 04 March 2014, 23:07:23 UTC updated expected output due to new processing profiles and env Here are the pairs of changes that were made: Oct 2012 Default Somatic Variation WGS Oct 2012 Default Somatic Variation WGS -- DV2 filter params bug fix Oct 2012 Default Somatic Variation Exome Oct 2012 Default Somatic Variation Exome -- DV2 filter params bug fix Oct 2012 Default Somatic Variation WGS (2762562) Oct 2012 Default Somatic Variation WGS -- DV2 filter params bug fix (b359413673b040d2b29b7810e71c4882) Oct 2012 Default Somatic Variation Exome (2762563) Oct 2012 Default Somatic Variation Exome -- DV2 filter params bug fix (ccdea755cabe46fb826394f6ba388ccc) https://gscweb.gsc.wustl.edu file:// 04 March 2014, 23:15:07 UTC
9425de5 Nathaniel Nutter 04 March 2014, 22:45:50 UTC use curl since it support file:// URLs 04 March 2014, 23:15:06 UTC
6bc6a8b Nathaniel Nutter 04 March 2014, 22:39:25 UTC use curl since it support file:// URLs 04 March 2014, 23:15:05 UTC
4bf08e3 Nathaniel Nutter 04 March 2014, 22:30:26 UTC use curl since it support file:// URLs 04 March 2014, 23:15:05 UTC
66ec893 Gue Su Chang 04 March 2014, 23:07:19 UTC Merge branch 'master' of ssh://git/srv/git/genome 04 March 2014, 23:07:19 UTC
bfdf8df Eddie Belter 04 March 2014, 22:19:42 UTC GM: create original genotpye VCF! 04 March 2014, 22:33:52 UTC
fffee3c Eddie Belter 04 March 2014, 22:19:14 UTC GM: update name of vcf file method 04 March 2014, 22:33:51 UTC
42fe08c Eddie Belter 04 March 2014, 21:58:27 UTC GM: excute build test uses test module 04 March 2014, 22:33:51 UTC
c489de5 Eddie Belter 04 March 2014, 21:57:51 UTC GM: rm setting ref, dbsnp and instdata to builds in test module 04 March 2014, 22:33:50 UTC
7f10049 Eddie Belter 04 March 2014, 21:24:41 UTC GM: update r/w test 04 March 2014, 22:33:50 UTC
d276aff Eddie Belter 04 March 2014, 21:23:01 UTC GM: update test for default csv headers 04 March 2014, 22:33:49 UTC
a294c12 Eddie Belter 04 March 2014, 21:22:10 UTC GM: rm expected genotypes from test module 04 March 2014, 22:33:49 UTC
1520584 Eddie Belter 04 March 2014, 21:21:21 UTC GM: updates to vcf helper and test 04 March 2014, 22:33:48 UTC
bdf46eb Eddie Belter 04 March 2014, 21:05:42 UTC GM: update extract to use factories 04 March 2014, 22:33:48 UTC
048e8cc Eddie Belter 04 March 2014, 21:05:13 UTC GM: fix getting info when decorating vcf entry; add test 04 March 2014, 22:33:47 UTC
037b361 Eddie Belter 04 March 2014, 19:22:01 UTC GM: use params fro build_reader; reader factory test uses test module 04 March 2014, 22:33:47 UTC
39bc084 Eddie Belter 04 March 2014, 19:10:19 UTC GM: use sampel_name instead of sample_id in default csv header 04 March 2014, 22:33:46 UTC
aad0b9d Eddie Belter 04 March 2014, 19:09:50 UTC GM: more read/write tests 04 March 2014, 22:33:46 UTC
2ffd4f9 Eddie Belter 04 March 2014, 19:08:17 UTC GM: factory to create entries 04 March 2014, 22:33:45 UTC
25a5abb Eddie Belter 04 March 2014, 19:04:12 UTC GM: read tsv returns a hash 04 March 2014, 22:33:45 UTC
c18654c Eddie Belter 27 February 2014, 23:20:18 UTC GM: set format to csv if separator is set in writer factory 04 March 2014, 22:33:44 UTC
365a873 Eddie Belter 27 February 2014, 23:19:29 UTC GM: update test objects 04 March 2014, 22:33:44 UTC
65761dd Eddie Belter 27 February 2014, 23:18:53 UTC GM: add next method as alias for read to read tsv 04 March 2014, 22:33:43 UTC
b810d23 Eddie Belter 27 February 2014, 23:18:24 UTC GM: updates to work w/ updated extract command 04 March 2014, 22:33:43 UTC
f180245 Eddie Belter 27 February 2014, 23:17:53 UTC GM: extract command tests 04 March 2014, 22:33:42 UTC
696e486 Eddie Belter 27 February 2014, 02:08:19 UTC GM: rm unused code from read write test 04 March 2014, 22:33:42 UTC
20c9bc7 Eddie Belter 27 February 2014, 02:07:25 UTC GM: rename info to vcf/csv helpers 04 March 2014, 22:33:41 UTC
44011f4 Eddie Belter 27 February 2014, 00:30:48 UTC GM: add format sample info to expected genotypes 04 March 2014, 22:33:41 UTC
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